call_macs2_merge_peaks: Calling MACS2 peak caller and merging resulting peaks

In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Calling MACS2 peak caller and merging resulting peaks

Description

Calling MACS2 peak caller and merging resulting peaks

Usage

call_macs2_merge_peaks(
  affectation,
  odir,
  p.value,
  format = c("scBED", "BAM")[1],
  ref,
  peak_distance_to_merge
)

Arguments

affectation	Annotation data.frame with cell cluster and cell id information
odir	Output directory to write MACS2 output
p.value	P value to detect peaks, passed to MACS2
format	File format, either "BAM" or "scBED"
ref	Reference genome to get chromosome information from.
peak_distance_to_merge	Distance to merge peaks

Value

A list of merged GRanges peaks

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.